Human collagenase-3 (MMP-13) is a member of the matrix metalloproteinase (MMP) family which includes the collagenases, stromelysins and gelatinases. The MMPs are involved in the degradation of the extracellular matrix and are associated with normal tissue remodeling processes such as pregnancy, wound healing, and angiogenesis. MMP expression and activity is highly controlled because of the degradative nature of these enzymes, where an apparent loss in MMP regulation results in the pathological destruction of connective tissue and the ensuing disease state. Accordingly, MMPs are a highly active set of targets for the design of therapeutic agents for the disease areas of arthritis and oncology (for reviews, see Woessner, J. F., FASEB 1991; Ries, C., and Petrides, E., Biol. Chem. Hoppe-Seyler 1995; Browner, M. F., Perspect. Drug Discovery Des. 1995; Morphy, et al., Curr. Med. Chem. 1995; and Zask, et al., Curr. Pharm. Des. 1996).
MMP-13 was identified on the basis of differential expression in normal breast tissues and in breast carcinoma. In addition, its expression has been reported in squamous cell carcinomas of the larynx, head and neck, in HCS-2/8 human chondrosarcoma cells, during fetal ossification, and in articular cartilage of arthritic patients.
There have been a number of X-ray and NMR structures solved for the catalytic domain of MMPs complexed with a variety of inhibitors (see e.g., Bode, et al., EMBO J. 1994; Gooley, et al., Nat. Struct. Biol. 1994; Lovejoy, et al., Science 1994; Lovejoy, et al., Ann. N.Y. Acad. Sci. 1994; Lovejoy, et al., Biochemistry 1994; Spurlino, et al., Proteins: Struct. Funct., Genet. 1994; Stams, et al., Nat. Struct. Biol. 1994; Becker, et al., Protein Sci. 1995; Gonnella, et al., Proc. Natl. Acad. Sci. U.S.A. 1995; Van Doren, et al., Protein Sci. 1995; Botos, et al., Proc. Natl. Acad. Sci. USA 1996; Broutin, et al., Acta Crystallogr., Sect. D: Biol. Crystallogr. 1996; Gooley, et al., J. Biomol. NMR 1996; Betz, et al., Eur. J. Biochem. 1997; Gonnella, et al., Bioorg. Med. Chem. 1997; and Moy, et al., Biochemistry 1998). There is a close similarity in the overall three-dimensional fold for these proteins consistent with the relatively high sequence homology (>40%). Despite this similarity in the MMP structures, there is a distinct substrate specificity between these enzymes indicative of specific biological roles for the various MMPs and a corresponding association with unique disease processes. One example of this potential specificity is the over-expression of MMP-13 in breast carcinoma and MMP-1 in papillary carcinomas. Therefore, the current paradigm in the development of MMP inhibitors is to design specificity into the structures of the small molecule instead of developing a broad spectrum MMP inhibitor (Birkedal-Hansen, et al., Crit. Rev. Oral Biol. Med. 1993; and Rockwell, et al., J. Am. Chem. Soc. 1996). The rationale behind this approach is that an inhibitor specific for the MMP uniquely associated with a disease process may potentially minimize toxic side effects. Therefore, extensive structural information for the various MMPs is critical for a structure-based approach in designing inhibitor selectivity (Birkedal-Hansen, et al., Crit. Rev. Oral Biol. Med. 1993; Rockwell, et al., J. Am. Chem. Soc. 1996; Ghose, et al., J. Am. Chem. Soc. 1995; Hajduk, et al., J. Am. Chem. Soc. 1997; and Olejniczak, et al., J. Am. Chem. Soc. 1997).
This concept has been facilitated by the extensive structural data available for the MMPs where a significant difference in the size and shape of the S1′ pocket has been observed (Moy, et al., Biochemistry 1998; Bode, et al., EMBO J. 1994; Gooley, et al., Nat. Struct. Biol. 1994; Lovejoy, et al., Ann. N.Y. Acad. Sci. 1994; Lovejoy, et al., Biochemistry 1994; Lovejoy, et al., Science 1994; Spurlino, et al., Proteins: Struct., Funct., Genet. 1994; Stams, et al., Nat. Struct. Biol. 1994; Becker, et al., Protein Sci. 1995; Gonnella, et al., Proc. Natl. Acad. Sci. U.S.A. 1995; Van Doren, et al., Protein Sci. 1995; Botos, et al., Proc. Natl. Acad. Sci. U.S.A. 1996; Broutin, et al., Acta Crystallogr., Sect. D: Biol. Crystallogr. 1996; Gooley, et al., J. Biomol. NMR 1996; Betz, et al., Eur. J. Biochem. 1997; and Gonnella, et al., Bioorg. Med. Chem. 1997). This structural difference across the MMP family provides an obvious approach for designing specificity into potent MMP inhibitors by designing compounds that appropriately fill the available space in the S1′ pocket while taking advantage of sequence differences. A number of examples have been previously reported using this approach where some selectivity between MMPs has been achieved by incorporating a biphenyl into the S1′ pocket (see e.g., Hajduk, et al., J. Am. Chem. Soc. 1997; and Olejniczak, et al., J. Am. Chem. Soc. 1997).
The inventors have determined both the solution and crystal structures of MMP-13, and, using rational drug design methods, have designed a novel, potent inhibitor that is highly selective for MMP-13.